The former prime minister of Kosovo, Ramush Haradinaj – who was acquitted by the war crimes tribunal in The Hague on Thursday 29 November after eight years under indictment and on trial – said on Saturday that he intends to "lead my country once again". The sitting prime minister has entered talks about standing down to make way for Haradinaj to return to office in early January.

In a highly charged accusation, Haradinaj said he believed his indictment to have been "the result of a deal in which I was a coin," between The Hague and the Serbian government. The accusation, levelled against former chief prosecutor Carla Del Ponte – currently the UN human rights investigator for Syria – is set to cause a major row.

Haradinaj was greeted back in the Kosovan capital, Pristina, by crowds of more than 100,000. "This has been another page in my long experience, and of our country and people," the former commander of the Kosovo Liberation Army during the war of independence told the Observer in an exclusive interview. "But now it is over. Our people have gone through great suffering, and now my plan is to become prime minister of Kosovo and build our society and economy for all Kosovans – Albanian, Serb, Roma, everyone."

Haradinaj was a leader of Kosovo's armed struggle in the late 1990s, but shifted quickly to politics. He was indicted after 100 days as prime minister, stepping down to offer himself for trial. "All along I have felt this was an injustice," he says. "All these years I've felt as though I was the coin in a deal made in Belgrade." He said he had been indicted as "a result of the trade-off that some have made with the Serbian government to make sure that Belgrade would extradite high-ranking Serbian war crimes suspects".

The acquittal also marks a potentially explosive moment across the Balkans. Addressing crowds, Haradinaj put the acquittal in a political context, declaring that it meant "our struggle was just and clean".

However, in Belgrade the director of Serbia's Kosovo office, Aleksandr Vulin, said the acquittal could sink negotiations over Kosovo. "How can we discuss the missing persons, victims and seized property if sitting opposite us is someone who was fairly charged with kidnappings and murders?" he asked.

But the Serbian prime minister, Ivica Dacic, counselled: "Despite everything, it is in Serbia's interests to continue the exchange with Pristina, because of EU integration."

Haradinaj insisted to the Observer: "There's no doubt that dialogue is the only way towards stability and democracy in the region and our country. Absolutely, the talks must continue."

Haradinaj's acquittal follows that of Bosnia's Nasir Oric – the commander in doomed Srebrenica – and recently that of Croatia's General Ante Gotovina, leaving in tatters the tribunal's strategy of "balanced" prosecution of all sides in the conflicts.

Haradinaj was indicted in March 2005 for his alleged connection to bodies dumped near a lake and his supposed role in torture and murder in the KLA camp at Jablanica. He was acquitted after a first trial, with the prosecution case collapsing for a number of reasons, including evidence that eight of the dead were last seen in the custody of Serbian forces. However, the court ordered a retrial, accepting a plea that witnesses may have been intimidated, and in order to present new ones. The new "evidence" was in turn exposed as fabricated and groundless.

The burning question as to why Haradinaj was indicted is now hugely controversial. One of Del Ponte's former senior prosecutors, Sir Geoffrey Nice, QC – lead attorney in the trial of former Serbian president Slobodan Milosevic – concurs with Haradinaj's notion of the "coin". "The prosecutor was clearly determined to prosecute Haradinaj," he said. "It may be that she was responding to complaints about an insufficient number of Kosovans being pursued.

"It was very clear that she would do a very great deal to get Karadzic and Mladic," he adds. "And when you step back and look at it all, you are going to ask: 'Are these things linked in a refined way?' It is one thing to say one is going to indict people from all sides in the conflict; the test of sufficiency of evidence to justify indicting someone has to remain the same. Prosecutors can not simply indict someone because they desperately want to see him indicted – or because someone else does."

In her memoir Del Ponte recalls Belgrade entwining the delivery of Mladic with Serbia's position on Kosovo – "refraining from placing Mladic under arrest," writes Del Ponte, "because Belgrade was going to exchange, for his handover, guarantees from the international community that Kosovo would remain part of Serbia". Del Ponte recalls how she responded to pressure from the Serbian prime minister Vojislav Kostunica by pledging him "one indictment by the end of the year [2004] against a high-level commander".

The commander who could deliver an independent Kosovo was Haradinaj, supported by the international community as the man to lead the new country.

When Haradinaj stood down, statesmen lined up to praise what current US vice-president Joseph Biden described as his "dignified departure". Biden said: "Serbian leaders in Belgrade privately acknowledge that of all Kosovan political leaders, it is Haradinaj with whom they could potentially negotiate with the greatest degree of confidence."

British foreign secretary Robin Cook lamented the loss of an "advocate of tolerance", as did the UN special representative to Kosovo, Soren Jessen-Petersen, at a time when "Kosovo is closer than ever before to achieving its aspirations".

However, "these were exactly the qualifications which made Haradinaj the man the Serbs had to get rid of in their bid to stifle a functioning independence for Kosovo," says his lawyer, Ben Emmerson QC.

The case was given to one of The Hague's most esteemed lawyers, Andrew T Cayley, QC. "It was a very difficult case to investigate on the ground," Cayley told the Observer, "harder than in any other place in the former Yugoslavia." But by 2004, Cayley said, he felt "under increasing pressure to come up with something … almost as if I was questioning a predetermined outcome.

"After a thorough review of the available evidence, I wrote an extensive report to the prosecutor saying that at that point we could not proceed on the evidence we had."

However, the report "was immediately suppressed inside the office. There was a lot of anger over my position and I was reprimanded. But I said: 'I have ethical, legal and moral responsibilities here.'" Cayley adds: "If this had been a domestic prosecution, there would have to have been a public inquiry."

Indeed, a former Director of Public Prosecutions, Lord Madonald of River Glaven QC, said yesterday: "This prosecution was a stupid attempt to equate resistance with aggression. It was an embarrassment to the international community."

The suppression of Cayley's report detonated a rebellion. Two senior prosecutors in Del Ponte's office, Sir Geoffrey and Mark Harmon – an American who has secured crucial convictions against perpetrators of the Srebrenica massacre – wrote to Del Ponte demanding that the indictment should have been subject to a peer review.

The two men said they were aware of sanctions threatened against "those who had concluded there was no case"; they considered that to proceed could entail "grave consequences in the region" and exacerbate what they called "the endemically unhappy atmosphere" in the prosecutor's office.

There was also international concern over the evidence. According to another memoir, by Del Ponte's spokeswoman Florence Hartmann, the US state department chargé d'affaires for Europe, Kathleen Stevens, asked: "Were your proofs given to you by Belgrade?" Other sources questioned whether the evidence had been "fabricated by Serbian intelligence services".

Ben Emmerson asks: "How could the prosecutor's office have relied so heavily on a file of evidence put together by the notorious Serbian intelligence service … then proceeded on these charges in the teeth of advice from its own senior lawyers that there was no case for Mr Haradinaj to answer?"

For the second trial, there were two witnesses: '80' and '81'. Witness 80 described a gruesome incident, but changed his story to say that Haradinaj was not there. But Cayley had, he says, "advised the prosecutor, in 2004, that Witness 80 was a wholly unreliable witness".

The evidence Witness 81 had given to his Serbian intelligence handler also collapsed. "The file had just been handed over by the Serbs to The Hague," says Emmerson. "The question is: who put him there and why?"

Del Ponte has not responded to the Observer regarding the allegation about a deal, but told the Tanjug agency in Belgrade she was "not surprised" by Thursday's verdict.

• This article was amended on 7 December 2012. The original stated that Kosovo's prime minister had stood down. This has been corrected.